Mass Effect 3: The Light In the Dark
by SiberskEsto
Summary: A new ending for the Mass Effect series, Commander Shepard must face down the Reaper horde, and come face to face with the galaxy's deadliest enemy; itself. Note: Indoctrination Theory not used.
1. Chapter 1

There was nothing.

Just a massive expanse of black oblivion that stretched out for miles.

But there were sounds.

Gunfire, radio chatter, the crackle and pop of a nearby fire, a dying engine, and screaming. There was a tremendous amount of screaming. But there was something else among the wails of the dying and the roar of weaponry. There was a name, a name that was called with a weak and guttural voice, the voice of a man who was nearing the end of his life.

"S-Shepard, SHEPARD!"

At the sound of his name, Shepard slowly opened his eyes, and stared at a sky as dark as he had ever seen. With all the strain he could muster, Shepard turned his neck towards the sound, feeling as though his neck was held down by a vice. What he saw was a man, a soldier, who was unmistakably clad in N7 armor. With further inspection, Shepard could see his legs were completely seared off at the knee, though they barely bled. The stumps had been cauterized, and the soldier leaned against the fiery remains of a hammer tank. "Shepard," he said, finally breaking the silence. "Thank God you're awake, thank G…" the soldier trailed off, and slid to the ground, dead. Even with cauterization, the trauma had been more than enough to finish him off. Shepard crawled next to the body, and tried his best to remember what had happened.

-[]-

The Crucible had finally been completed. The salvation of Earth, as well as the salvation of all sentient life now stood within reach, as the great technological obelisk entered Earth's orbit. The

Reapers had started to barrel down on the tiny blue planet, and it was only a matter of time before the sheer force of their might threatened to eliminate all trace of the human race from the galaxy. Shepard, as well as what was left of Earth's defense, had fought tooth and nail to reach the Citadel beam, which was the only way they could reach the Citadel, open the arms, and combine it with the device and end the Reaper threat once and for all. However, Murphy's Law

constantly loomed like a malevolent shadow, just waiting for the precise moment to strike. And strike it did, right when Shepard and the rest of Hammer, led by Captain Anderson, reached the hilltop overlooking the Citadel beam. In their path stood Harbinger, the de facto leader of the Reaper assault and the continued bane of Shepard's existence. Perhaps against their better judgment, Shepard led Hammer down the hill in what could only be described as a suicide run. Harbinger was unperturbed, and simply fired with calculated and deadly beams of pure energy, which decimated the Hammer tanks. Commander Shepard was skilled enough to avoid these blasts for the most part, until a seemingly deliberate pillar of destructive force came barreling down right in front of him. Nimble as ever, Shepard avoided the beam, but had not counted for the sheer heat and force coming off of it. His armor was violently burned, with his only saving grace being the holographic tech armor he had over his body.

-[]-

Now Shepard was all but broken, covered with the shredded remnants of the durable polymer under weave that made up the backbone of all N7 armor, as well as his own blood. The sensation Shepard felt could best be described as being crushed by a large mechanical press, whose surface was blazing hot. Amid his complete disorientation and overwhelming pain, the ever resilient Commander could make out the blinding glow of what could only be the Citadel beam. Rising slowly, Shepard began the long, painful trek to the beam. Even if he died upon arrival, he could not give up on his mission. He had barely taken ten steps when he heard the all too familiar hiss and groan of what had to be a Husk. Shepard groaned upon the realization, and cursed loudly when a small platoon of the corrupted monsters emerged from the swamp of twisted metal and flame. As an added bonus, a corrupted Turian, a Marauder, emerged with them, almost flanking their approach. Ever indignant against the chaotic winds of fate, Shepard lifted his standard issue pistol and pointed meekly at the oncoming horde, convinced he did not have enough thermal clips to keep him from dying instantly. As the monsters grew ever closer, they were suddenly cut down by a barrage of compacted energy projectiles. It took all of thirty seconds to dispose of the entire group, and when the dust had settled, Shepard turned to meet his savior. Behind a standard military turret, with burning eyes and a grizzled face, stood the imposing figure of Captain David Edward Anderson.

-[]-

"Anderson!" Shepard managed to cough out, his elation making him ignore the obvious fact that he could have been caught in the crossfire. "You're still alive?"

"Give me more credit than that Shepard" said Anderson, tough as ever but obviously tired. "You may be the savior of the galaxy, but I've just spent the last month or so practicing how to pull my ass out of the fire."Shepard supported himself with a nearby tank hull, not wanting to collapse in front of his old friend and commanding officer, who approached him now with all the fire of a man possessed.

"What's the situation?"

"Hammer has been completely wiped out, no survivors. Where's Harbinger?"

"Gone. He did a quick survey of the area before heading skyward, presumably towards the Citadel."

This was not good news, but Shepard knew there was no more time to waste.

"Anderson, we need to get to the beam. You're in much better condition than I am so you should go first. I'll try my best to rendezvous with you at the Citadel." "Understood," Anderson replied, placing a small communications device in Shepard's palm. "In case we get separated" Anderson said running towards the beam. "See you on the other side!" Shepard took a moment to catch his breath, subsequently placed the device in his ear, and entered the beam, disappearing in a flash of light.


	2. Chapter 2

As expected, it was not a pleasant journey up the beam. Shepard felt as if he was going through a Mass Relay personally, instead of with a ship. While he knew the trip only took a few seconds, it felt like an eternity. Finally, his journey came to its end, and a barely conscious Shepard arrived at the Citadel. Or, at least what was left of it. The area where he emerged was covered in a dark red hue, as shredded pieces of metal and bits of wire hung from the walls. However, that paled in comparison to the number of bodies. Human, Batarian, Turian, Asari, it didn't matter. Their bodies lay contorted and mangled all over the now blood stained steel floor.

No one looked to be indoctrinated; they were all still in their original bodies, free of the technological "implants" the Reapers had used so far. In the dark crimson light, surrounded by the bodies of those unfortunate enough to not have escaped, it was the closest Shepard felt he had come to hell. His thoughts were interrupted by a sudden detection of movement, and Shepard steeled his nerves, raising his pistol in the direction of the sound. He was ready to fire when out emerged the unmistakable greenish tint of a Keeper, insect in appearance but without any sentience. Shepard sighed and trudged forward, determined to see his mission through.

-[]-

There were no other threats present on the Citadel, to Shepard's relief. Instead, it was deathly quiet, a sharp contrast to the cacophony of noise that the Citadel was known for. With nothing else to go by, Shepard tried the communications device he had received from Anderson.

"Anderson, this is Shepard, where are you?"

Static.

"Anderson, I repeat, this. is. Shepard."

This time, there was a reply. "Shepard?" the voice was mangled by some sort of jamming signal, and Shepard found himself struggling to discern the words from the buzz.

"Anderson? I read you, but barely. Where are you?"

"Some..sort..of..giant room. There seem to be some door controls behind me. I'll open the doors and hope you can see it."

To Shepard's surprise, there was a huge opening a few feet from him, and he shambled forward towards the light. There, in what seemed to be some sort of great hall, stood Captain Anderson, situated in front of what seemed to be a control panel. "Shepard! Glad you could make it. I was just ab…" Anderson's words were cut short by the thundering noise of a gunshot. Anderson, momentarily clutching his stomach and seeing blood, stumbled backwards onto the floor. "Anderson!" Shepard cried, and just as quickly fell over, feeling another bullet rip through his own leg. As Shepard turned to face their aggressor, he could distinctly make out the impression of a dark black suit, punctuated by the brilliant hue of cybernetically enhanced eyes.

-[]-

The Illusive Man, former leader of the now defunct Cerberus faction, emerged from the darkness, wielding a still smoking pistol in one hand and tossing away a used cigarette in the other. The Illusive Man had brought Shepard back to life, and had supplied the necessary resources Shepard needed to combat and destroy the Collectors, indoctrinated Protheans under Reaper control, who were harvesting human lives in order to expand the Reaper forces. However, with the revelation that the Illusive Man desired control over the Reapers as opposed to their destruction, a schism had occurred, and now instead of just fighting the Reapers, Shepard and the rest of Earth's forces now had to contend with Cerberus forces as well. This culminated in a full scale attack on Cerberus headquarters, which ended with Cerberus destroyed but with the Illusive Man's escape. At least, until now.

-[]-

"Your resilience never ceases to amaze me Shepard, but if you can't count on the will of a man who came back from the dead than what can you count on?" The Illusive Man still held that smug sense of superiority, that all too apparent tone that betrayed just how self-centered he really was. "If you're wondering why I'm here, let's just say no one really checks for IDs when the entire galactic fleet is situated in one location. All I had to do was hide behind the groups of dead bodies and follow you, and suddenly here I am, right where I need to be to bring about humanity's greatest triumph." Shepard sneered but was incapable of retaliation, as that leg wound proved to be one bullet too many. The Illusive Man simply stepped over Shepard's body and hovered over Anderson's. "Pity about the Captain, he really was one of those rare men who emerge ever so often in the galaxy. But I need to even out my odds; I couldn't very well expect to take on the both of you in a fair fight."

Shepard remained silent.

"It's all as it should be, don't you think? The world's going to oblivion and I can finally grasp the power I need to deliver it."

"If you think I'm going to let you…"

"Enough with the heroics Shepard, it is beneath the both of us. I think if we can agree on anything is that the ideals of right and wrong don't apply to us anymore. We both know that in order to save what we care about, expediency trumps morality."

"You don't care about anything if it doesn't satisfy your own goals, and the minute we start abandoning our morals is the minute we are no better than the Reapers."

The Illusive Man smirked, almost burst out laughing "Really Shepard? That tired old diatribe is your only rebuttal? Surely being alive this long has granted you better sense than that?"

"It's all the sense I need."

"Yes, well, we grown ups have to recognize when it is time to step out the little land of idealism and face facts. Morality doesn't apply to the Reapers. Put a jury out in front of them and they'll simply blast them away. Or, more likely, indoctrinate them into saying they're innocent. Right and wrong don't exist because we want them to; they were invented by tired old men thousands of years ago who were too afraid of losing their own power to see the big picture. And that's what it all boils down to doesn't it Shepard? Power. Sheer, unadulterated power. Power is the reason the Reapers decimate all who stand before them. Power is the reason why the Krogans were nearly exterminated all those years ago. Power decides what is "right" and what is "wrong" and power is what will allow me to save mankind."

"And it is in my power to say that moral nihilism is overplayed. I think what you are doing is wrong, and it is that power that is going to help me stop you."

The Illusive Man seemed to lose patience "As stimulating as these discussions of ours tend to be Shepard, I cannot do anything if you simply refuse to see the point. I have a galaxy to save and you're busy arguing semantics and tossing out petty insults. They should have put an ugly VI of ME in the Citadel." The Illusive Man stepped forward, placing the pistol in direct line with Shepard's head. "Goodbye Shepard, go to your grave knowing the fate of all sentient life rests within capable hands."

Shepard closed his eyes. Gunshot. Blood splatter.

-[]-

end of part two. stick around for part 3, and please leave your comments in the review section.


	3. Chapter 3

What is death to a man?

For many, death carries an unspoken, yet at the same time unmistakable fear around it. The idea that all beings, regardless of status or behavior, will eventually die is frightening. For others, there is the idea that death is inevitable, and therefore fearing it amounts to little more than wasted time. But what of Commander Shepard? He boasted a claim that perhaps no other being in the galaxy had; he had conquered death. Death, REAL death, had embraced Shepard in the cold, dark reaches of space. Yet through the graces of modern technology Shepard's otherwise lifeless body breathed life once more, and with that body Shepard had eliminated the galaxy's biggest threats. So what did Shepard feel when it came to death? What SHOULD he have felt towards death? Should he fear it? No. He had conquered it, and conquest eliminates the need for fear. Should he accept it? The answer was also no. Pure instinct told Shepard what the Reapers were: a threat. Not something to be feared, not something to be hated, but something that needed to be destroyed. Now, with the Illusive Man pointing a gun at him, willing and able to end his life at a moment's notice, Shepard had come to that very crossroad. Should he fear the Illusive Man, and the gun that he wielded? Or should he submit to it, allow it to kill him, and accept the fact that the Reapers were either going to kill them all of their own will, or under the Illusive Man's? But Shepard never had an eye for philosophy. Action came naturally to him, and this case was no different. And so, allowing no alternative to breach his thoughts, Shepard lunged.

[]

The Illusive Man had been so taken aback by the suddenness of Shepard's actions that the ensuing gunshot happened purely by chance, and had pierced Shepard's shoulder. But momentum submitted under Shepard's will and had guided him crashing into the Illusive Man and onto the cold, metal floor. Both men now tussled among each other, looking almost like a schoolyard altercation as opposed to a galaxy deciding struggle. Neither men relented, their respective wills guiding every punch, every unfocused grab.

"Damn you Shepard!" The Illusive Man cried, his previous smug demeanor giving way to pure hatred. "Why. Won't. you. FALL?"

"You first" replied Shepard, and with that he used both legs to push the Illusive Man back enough steps to fall right into the arms of a staggering Captain Anderson, who received his "gift" with an unceremonious right hook to the jaw.

"It's no gunshot, but I hope that stung you bastard" said Anderson, and the Illusive Man stumbled onto the floor. Now, like a rat trapped between a wall and a cobra, The Illusive Man had nowhere to go.

"DON'T YOU REALIZE WHAT EITHER OF YOU ARE DOING?" he cried. "Think of all the progress you're stifling, the innovation you're turning away!"

Shepard limped over to the Illusive Man, the blood from his shoulder pouring down and mixing with the other wounds. "Illusive Man, we've conquered space and have traveled to places previously thought nonexistent by even the brightest of our minds. I think in context, progress and innovation can wait a little while."

[]

By all accounts, the Illusive Man had been beaten, his plans foiled. But when a man cannot conquer, he destroys. The Illusive Man pulled out a single flash bang grenade, harmless in any other situation. But with all three men gathered so closely together, and standing on such a narrow crosswalk, the "bang" would send all three tumbling to their deaths.

"Back away, the both of you!" The Illusive Man said, nearly starting to foam at the mouth. "If I kill the three of us, nothing gets resolved! Now I am willing to allow the both of you to escape, granted you leave me to my own devices."

Both Shepard and Anderson were in no condition to spring for the gun that was only a few feet away, and both knew the Illusive Man would make the most of his threat. Anderson looked at Shepard, who could barely return it.

"Tell them what happened here Shepard." Anderson said, cracking a smile that usually belongs to men much older and wiser. "Tell them what happened and don't you dare make me sound like a hero." And with that, Anderson broke into a full running tackle, which gave The Illusive Man enough time to activate the grenade but not throw it, and sent both men careening over, punctuated by a small, white hot burst, not unlike the kind a star makes when it dies.

[]

It all happened so quickly that Shepard could not hope to immediately act, and when the full weight of what happened hit him, he could only slump to the floor, pounding meekly on the steel. But this war had taught Shepard that sacrifices were not made to be mourned; they were made to be honored. And with the voice of his Captain still fresh in his ear, he activated the door controls, and the giant arms of the Citadel creaked open with a roar.

[]

Admiral Hackett had been watching the Citadel closely, waiting for the precise moment for the arms to open. This was no small feat, as he also had to coordinate the attack on the Reaper armada. Just as he was about to start devising a new plan, he saw the massive arms of the Citadel open, and nearly lost his voice screaming the order to move forward.

[]

Shepard could see the Crucible come closer, ready to align itself with the Citadel's core and bring about the salvation of sentient life. All of the sacrifices that were made, all of the death, the sadness, the sleepless nights were finally going to be answered for, and it would all end. For the longest time he could remember, Shepard was going to be able to rest. This thought was still in his head when he heard a massive, metallic groan, and the thought was soon banished when he saw that the Crucible had stopped completely, being held stationary in the arms of a massive Reaper, whose core had an orange glow that pierced the dark sky.

Apologies to all those who have been reading this story for such a long delay. The conclusion and epilogue will be uploaded as soon as I can.


End file.
